The party’s head of data and technology, Chris Jones, has created the website organise.scot.
The website was registered in July last year.
Mr Jones had also previously registered two pro-independence websites – ref.scot and mobilise.scot – for the party.
First Minister Nicola Sturgeon has said the SNP is using every power at its disposal to deliver for the people of Scotland.
She claimed just days ago the full potential of Scotland could only be seen when the nation was independent.
The website was bought after Ms Sturgeon told the Scottish Parliament she had “reset” her referendum timetable.
The timetable rejig has come in the wake of the SNP losing 21 of its 56 seats in June’s snap election.
SNP chief executive Peter Murrell confirmed the website’s registration on Twitter, but stressed the process had cost just £24 and was not a new website.
Scottish Conservative deputy leader Jackson Carlaw told The Herald newspaper: “This shows that while Nicola Sturgeon was pretending to the people of Scotland she was pausing the independence agitation, her party machine was doing the very opposite.
“Despite accepting the voters didn’t want another referendum, her IT elves were busy building the online foundation for another push.
“No matter what the nationalists say in public, they will never be able to let go in private.”
Opposition parties have claimed Ms Sturgeon will push for Indyref2 in the autumn.
The First Minister first announced her desire to hold a second referendum in March last year.
Mr Jones has been the SNP’s head of data and technology since December 2014.
He registered ref.scot and mobilise.scot for the SNP in March and June respectively last year.
The registration was reportedly completed by Mr Jones using his personal email and home address rather than his official SNP credentials.
An SNP spokesperson said: “We’ll let Jackson Carlaw in on a wee secret – the SNP has been campaigning for an independent Scotland since the 1930s.”